Alpha-fetoprotein (AFP) and albumin are related proteins, which contain about 585 amino acid residues that are organized in a characteristic structure of 3 homologous domains of about 195 amino acid residues. We have compared the domains of mouse, rat, and human AFP and rat, bovine, and human albumin using computer programs designed to quantify relationships between proteins. The comparisons of corresponding domains of the AFPs (e.g. domain I of rat and human AFP) reveal that each domain is well conserved. Similar results were found for the comparisons of corresponding domains in the albumins. In contrast, there was much less similarity between corresponding domains of albumin and AFP. These comparisons between AFP and albumin revealed that : (1) the amino acid sequences in domain III, which is at their carboxy terminus, are most conserved, and (2) the amino acid sequences in domain I, which is at their amino terminus, are least conserved. This suggests that there are differences in the constraints on amino acid substitutions among the domains of AFP and albumin during the approximately 400 million years since they diverged from a common ancestor. Also, computer studies revealed that there are substantial differences between domains I, II, and III in each AFP and albumin species, which indicates that these domains are significantly different from their ∼ 195 residue ancestral domain. Finally, we find that mouse and rat AFP are more dissimilar to the albumins than is human AFP. Overall, our computer analyses indicate that AFP and albumin can be considered to be composed of distinct, but related, ∼ 195 residue proteins, each of which could differ in some of their properties; for example, the binding of fatty ac